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Anatoly B. Kolomeisky

Professor of Chemistry and Professor of Chemical and Biomolecular Engineering

Theoretical investigation of complex chemical and biophysical processes using the methods of statistical mechanics. Specific projects: 1) motor proteins; 2) cytoskeleton filaments; 3) polymer translocation through nanopores; 4) facilitated diffusion; 5) transport through membrane pores; 6) multi-partical non-equilibrium dynamics; 6) protein nucleation and crystallizations; 7) viscosity in biological systems, 8) protein-DNA interactions, 9) modeling of dynamics of nanocars.

Publications

 Dissecting the Effect of Morphology on the Rates of Singlet Fission: Insights from Theory, X. Feng, A.B. Kolomeisky and A.I. Krylov, J. Phys. Chem. C, 118, 19607-19617 (2014).

A Simple Kinetic Model for Singlet Fission: A Role of Electronic and Entropic Contributions to Macroscopic Rates, A.B. Kolomeisky, X. Feng and A.I. Krylov, J. Phys. Chem. C 118, 5188-5195 (2014). 

A New Theoretical Approach to Analyze Complex Processes in Cytoskeleton Proteins, X. Li and A.B. Kolomeisky, J. Phys. Chem. B 118, 2966-2972 (2014).

Bulk Induced Phase Transitions in Driven Diffusive Systems, Y.-Q. Wang, R. Jiang, A.B. Kolomeisky and M.-B. Hu, Sci. Rep. 4, 5459 (2014).  

Development of Morphogen Gradient: The Role of Dimension and Discreteness, H. Teimouri and A.B. Kolomeisky, J. Chem. Phys. 140, 085102 (2014).

M.N. Artyomov, A.Y. Morozov and A.B.Kolomeisky, "Dynamics of Molecular Motors in Reversible Burnt-Bridge Models,"  Condens. Matter Phys. 13, 23801 (2010).

R.K. Das and A.B. Kolomeisky, "Facilitated Search of Proteins on DNA: Correlations are Important," Phys. Chem.-Chem. Phys. 12, 2999-3004 (2010).

J. Lin, A.B.Kolomeisky and A. Meller, "Helix-Coil Kinetics of Individual Polyadenylic Acid Molecules in a Protein Channel,"   Phys. Rev. Lett. 104, 158101 (2010).

Pathway Structure Determination of Complex Stochastic Networks with Non-Exponential Dwell Times, X. Li, A.B. Kolomeisky and A. Valleriani, J. Chem. Phys. 140, 184102 (2014).

Positive and Negative Impacts of Nonspecific Sites During Target Location by a Sequence-Specific DNA-binding Protein: Origin of the Optimal Search at Physiological Ionic Strength, A. Esadze, A.B. Kolomeisky and J. Iwahara, Nucl. Acids Res. 42, 7039-7046 (2014).

Stochastic Kinetics on Networks: When Slow is Fast, X. Li, A.B. Kolomeisky and A. Valleriani, J. Phys. Chem. B, 118, 10419-10425 (2014).

Unveling the Hidden Structure of Complex Stochastic Biochemical Networks, A. Valleriani, X. Li and A.B. Kolomeisky, J. Chem. Phys. 140, 064101 (2014). 

H. Teimouri and A. B. Kolomeisky All-Time Dynamics in Complex Continuous-Time Random Walk Models.  J. Chem. Phys., 138 2013: 084110

K. Uppulury, A. K. Efremov, J. W. Driver, D. K. Jamison, M. R. Diehl and A. B. Kolomeisky Analysis of Cooperative Behavior in Multiple Kinesins Motor Protein Transport by Varying Structural and Chemical Properties .  Cell. Mol. Bioeng., 6 2013: 38-47

X. Banquy, G. W. Greene, B. Zappone, A. B. Kolomisky and J. N. Israelachvili Dynamics of Force Generation by Confined Actin Filaments.  Soft Matter, 9 2013: 2389-2392

B. Farrell, F. Qian, A. B. Kolomeisky, B. Anwari and W. E. Brownell Measuring Forces at the Leading Edge: A Force Assay for Cell Motility.  Integr. Biol., 5 2013: 204-214

X. Li and A. B. Kolomeisky Mechanisms and Topology Determination of Complex Chemical and Biological Network Systems from First-Passage Theoretical Approach.  J. Chem. Phys., 139 2013: 144106

A. B. Kolomeisky Mechanisms of Protein Binding to DNA: Statistical Interactions are Important.  Biophys. J., 104 2013: 966-967

A. B. Kolomeisky Motor Proteins and Molecular Motors: How to Operate Machines at the Nanoscale.  J. Phys.: Condens. Matter, 25 2013: 463101

R. Jiang, Y.-Q. Wang, A. B. Kolomeisky, W. Huang, M.-B. Hu and Q.-S. Wu Phase Diagram Structures in a Periodic One-Dimensional Exclusion Process.  Phys. Rev. E, 87 2013: 012107

A. B. Kolomeisky Physics of Protein Motility and Motor Proteins. .  J. Phys.: Condens. Matter, 25 2013: 370301

A. Veksler and A. B. Kolomeisky Speed-Selectivity Paradox in the Protein Search for Targets on DNA: Is It Real or Not?.  J. Phys. Chem. B, 117 2013: 12695-12701

P.-L. E. Chu, L.-Y. Wang, S. Khatua, A. B. Kolomeisky, S. Link and J. M. Tour Synthesis and Single-Molecule Imaging of Highly Mobile Adamantane-Wheeled Nanocars.  ACS Nano, 7 2013: 35-41

X. Li and A. B. Kolomeisky Theoretical Analysis of Microtubules Dynamics Using a Physical-Chemical Description of Hydrolysis.  J. Phys. Chem. B, 117 2013: 9217-9223

D. Panja, G. T. Barkema and A. B. Kolomeisky Through the Eye of the Needle: Recent Advances in Understanding Biopolymer Translocation.  J. Phys.: Condens. Matter, 25 2013: 413101

A. V. Akimov, C. Williams and A. B. Kolomeisky Charge Transfer and Chemisorption of Fullerene Molecules on Metal Surfaces: Application to Dynamics of Nanocars.  J. Phys. Chem. C, 116 2012: 13816-13826

K. Uppulury, A. K. Efremov, J. W. Driver, D. K. Jamison, M. R. Diehl and A. B. Kolomeisky How the Interplay between Mechanical and Nonmechanical Interactions Affects Multiple Kinesin Dynamics.  J. Phys. Chem. B, 116 2012: 8846-8855

A. B. Kolomeisky and A. Veksler How to Accelerate Protein Search on DNA: Location and Dissociation.  J. Chem. Phys., 136 2012: 12501

A. B. Kolomeisky and D. Lacoste Random Hydrolysis Controls the Dynamic Instability of Microtubules.  Biophys. J., 102 2012: 1274-1283

A. V. Akimov and A. B. Kolomeisky Unidirectional Rolling of Nanocars Induced by Electric Field.  J. Phys. Chem. C, 116 2012: 22595-22601

J. H. P. Schulz, A. B. Kolomeisky and E. Frey Current Reversal ad Exclusion Processes with History-Dependent Random Walks.  Europhys. Lett., 95 2011: 30004

A. V. Akimov and A. B. Kolomeisky Dynamics of Single-Molecule Rotations on Surfaces that Depend on Symmetry, Interactions and Molecular Sizes.  J. Phys. Chem. C, 115 2011: 125-131

A. B. Kolomeisky Formation of a Morphogen Gradient: Acceleration by Degradation.  J. Phys. Chem. Lett., 2 2011: 1502-1505

A. B. Kolomeisky and K. Uppulury How Interactions Control Molecular Transport in Channels.  J. Stat. Phys., 142 2011: 1268-1276

A. B. Kolomeisky Michaelis-Menten Relation for Complex Enzymatic Networks.  J. Chem. Phys., 134 2011: 155101

A. V. Akimov and A. B. Kolomeisky Molecular Dynamics Study of Crystalline Molecular Gyroscopes.  J. Phys. Chem. C, 115 2011: 13584-13591

I. V. Kupchenko, A. A. Moskovsky, A. V. Nemukhin and A.B.Kolomeisky On the Mechanism of Carborane Diffusion on a Hydrated Silica Surface.  J. Phys. Chem. C, 115 2011: 108-111

A. B. Kolomeisky Physics of Protein-DNA Interactions: Mechanisms of Facilitated Diffusion.  Phys. Chem. Chem. Phys., 13 2011: 2088-2095

J. W. Driver, D. K. Jamison, K. Uppulury, A. R. Rogers, A. B. Kolomeisky and M. R. Diehl Productive Cooperation among Processive Motors Depends Inversely on Their Mechanochemical Efficiency.  Biophys. J., 101 2011: 386-395

A. V. Akimov and A. B. Kolomeisky Recursive Taylor Series Expansion Method for Rigid-Body Molecular Dynamics.  J. Theor. Chem. Comp., 7 2011: 3062-3071

R. Wang, A. B. Kolomeisky, and M. Liu Spontaneous Symmetry Breaking on a Multiple-Channel Hollow Cylinder.  Phys. Rev. A, 375 2011: 318-323

J. W. Driver, A. R. Rogers, D. K. Jamison, R. K. Das, A. B. Kolomeisky and M. R. Diehl Coupling between Motor Proteins Determines Dynamic Behaviors of Motor Protein Assemblies.  Phys. Chem. Chem. Phys., 12 2010: 10398-10405

S. S. Konyukhov, I. V. Kupchenko, A. A. Moskovsky, A. V. Nemukhin, A. V. Akimov and A. B. Kolomeisky Rigid-Body Molecular Dynamics of the Fullerene-Based Nanocars on the Metallic Surfaces.  J. Chem. Theory Comput., 6 2010: 2581-2590

A. B. Kolomeisky Continuous-Time Random Walks at All Times.  J. Chem. Phys., 131 2009: 23414

R. K. Das and A. B. Kolomeisky Dynamic Properties of Molecular Motors in the Divided-Pathway Model.  Phys. Chem. Chem. Phys., 11 2009: 4815-4820

C. H. Sykes, A. Akimov and A. B. Kolomeisky Dynamics of Thioethers Molecular Rotors: Effect of Surface Interactions and Chain Flexibility .  J. Phys. Chem. C, 113 2009: 10913-10920

S.Khatua, J.M. Guerrero, K. Claytor, G. Vives, A.B. Kolomeisky, J.M. Tour and S. Link Micrometer-Scale Translation and Monitoring of Individual Nanocars on Glass .  ACS Nano, 3 2009: 351-356

D. Panja, G. T. Barkema and A. B. Kolomeisky Non-Equilibrium Dynamics of Single Polymer Adsorption to Solid Surfaces.  J. Phys. Condens. Matter, 21 2009: 242101

A. Mohan, A. B. Kolomeisky, M. Pasquali Effect of Charge Distribution on the Translocation of an Imhomogeneously Charged Polymer Through a Nanopore.  J. Chem. Phys., 128 2008: 125104-1:125104-7

A. B. Kolomeisky, S. Kotsev Effect of Interactions on Molecular Fluxes and Fluctuations in the Transport across Membrane Channels.  J. Chem. Phys., 128 2008: 085101-1:185101-6

A. B. Kolomeisky How Proteins Translate Through Pores: Memory is Important.  Biophys. J., 94 2008: 5547-1548

K. Tsekouras and A. B. Kolomeisky Inhomogeneous Coupling in Two-Channel Asymmetric Exclusion Processes.  J. Phys. A: Math Theor., 41 2008: 095002

R. K. Das, A. B. Kolomeisky Interaction between Motor Domains Can Explain the Complex Dynamics of Heterodimeric Kinesins.  Phys. Rev. E, 77 2008: 061912

A. Akimov, A. V. Nemukhin, A. Moskovsky, A. B. Kolomeisky, J. M. Tour Molecular Dynamics of Surface-Moving Thermally Driven Nanocars.  J. Chem. Theor. Comp., 4 2008: 652-656

M. N. Artyomov, A. Y. Morozov, A. B. Kolomeisky Molecular Motors Interacting with Their Own Tracks.  Phys. Rev. E, 77 2008: 040901(R)

A. G. Cherstvy, A. B. Kolomeisky, A. A. Kornyshev Protein-DNA Interactions: Reaching and Recognizing the Targets.  J. Phys. Chem. B, 112 2008: 4741-4750

R. K. Das, A. B. Kolomeisky Spatial Fluctuations Affect the Dynamics of Motor Proteins.  J. Phys. Chem. B, 112 2008: 11112-11121

Kolomeisky Research Group
Anatoly Kolomeisky

  • M.S. Chemistry (1991) Moscow State University
  • M.S. Chemistry (1996) Cornell University
  • Ph.D. Chemistry (1998) Cornell University
  • Center for Theoretical Biological Physics
  • Department of Chemical and Biomolecular Engineering
  • Institute of Biosciences and Bioengineering
  • Rice Quantum Institute
  • Theoretical Physical Chemistry. Theoretical Biophysics. Statistical Mechanics of Complex Systems. Biological Transport. Thermodynamics of Electrolytes. Random Walks. Theory of Hydrophobicity.
Email: tolya@rice.edu
Phone: (713) 348-5672
Office: Anderson Biological Lab, 306